New upstream version 4.6.5

CONFIG ?= fltk-config

PDF_PS_FLAGS ?= -DNO_PDF

EXTRALIBS = `$(CONFIG) --use-images --ldflags` -ldl -lpthread -lz

EXTRALIBS = `$(CONFIG) --use-images --ldflags`

CC = gcc

CXX = g++

           HOW TO COMPILE SEAVIEW ON UNIX/LINUX SYSTEMS

The seaview program requires the FLTK library for its graphical user interface.

Version 1.3.0 or later of FLTK is necessary.

The FLTK library is available as packages for a number of Linux distributions.

If this package is installed on your system, go to step II.

If no such package is available for your system, or if version 1.3.0 is not available,

or if you don't want to use such package, you can compile the FLTK library as follows.

I COMPILING THE FLTK LIBRARY FROM SOURCE

========================================

The source code of the FLTK library is available at the "Download" item of http://www.fltk.org/.

- Get the stable release source archive, currently fltk-1.3.3-source.tar.gz

- Compile the FLTK library on your system:

   cd fltk-1.3.3

   ./configure

   make

It's not necessary to do "make install".

II COMPILING THE SEAVIEW PROGRAM

================================

First unpack the seaview source archive (seaview.tar.gz).

IIa Preparing the seaview makefile

If the FLTK library is installed on your system (i.e., include files in /usr/include/FL,

and libraries at /usr/lib/libfltk*), go to step IIb.

Otherwise, edit Makefile from the seaview source directory which contains these 5 lines:

#to use your own, uninstalled FLTK library,

#uncomment the next 3 lines and adapt the 1st to your local file system 

#FLTK = $(HOME)/fltk-1.3

#IFLTK = -I$(FLTK)

#CONFIG = $(FLTK)/fltk-config

Transform these lines into:

#to use your own, uninstalled FLTK library,

#uncomment the next 3 lines and adapt the 1st to your local file system 

FLTK = $(HOME)/fltk-1.3

IFLTK = -I$(FLTK)

CONFIG = $(FLTK)/fltk-config

and also change the FLTK = $(HOME)/fltk-1.3 line so it gives the location in your system

of the top of the FLTK source tree.

IIb Compile/link the seaview program

In the seaview source directory, run

make

III Install seaview external programs

=====================================

Seaview drives 4 external programs (clustalo, muscle, Gblocks, phyml). Linux executables

of these are available from the linux items of http://pbil.univ-lyon1.fr/software/seaview.html

They are also available as packages of most Linux distributions.

These programs should be put in your PATH or in the same directory as the seaview

executable for seaview to drive them.

By default seaview searches for the phyml executable under the names PhyML-3.1_linux32

or PhyML-3.1_linux64. If they are installed under other names on your system, seaview 

will ask you for their name and location which are remembered for subsequent runs.

  set_seaview_modified(target, TRUE);

}

void store_concat_part_as_region(SEA_VIEW *target, char *name, int from, int to)

{

  list_segments ls = {from, to, NULL};

  list_segments *pls = new list_segments; *pls = ls;

  region *r = new region;

  r->name = strdup(extract_filename(name));

  r->list = pls;

  list_regions *list = target->regions;

  list_regions *list2 = new list_regions;

  list2->element = r;

  list2->next = NULL;

  if (list) {

    while (list->next) list = list->next;

    list->next = list2;

  } else target->regions = list2;

}

void concatenate_no_gui(int argc, char *argv[])

{

  char *err_message;

  bool std_output = false;

  SEA_VIEW *target = cmdline_read_input_alignment(argc, argv);

  bool record_partition = isarg(argc, argv, "-record_partition");

  if (record_partition) store_concat_part_as_region(target, argv[argc-1], 1, target->seq_length);

  char *all_sources = argname(argc, argv, "-concatenate");

  known_format out_format = target->format_for_save;

  bool is_by_rank = isarg(argc, argv, "-by_rank");

  while (source_name) {

    SEA_VIEW *source = cmdline_read_input_alignment(1, &source_name);

    int old_length = target->seq_length + 1;

    concatenate(target, source, !is_by_rank, !is_by_rank, true);

    if (record_partition) store_concat_part_as_region(target, source_name, old_length, target->seq_length);

    source_name = strtok(NULL, ",");

    }

<?xml version="1.0" encoding="UTF-8"?>

<!-- Copyright 2015 Manolo Gouy <manolo.gouy_at_univ-lyon1.fr> -->

<component type="desktop">

 <id>seaview.desktop</id>

 <metadata_license>CC0-1.0</metadata_license>

 <project_license>GPL-3.0</project_license>

 <name>SeaView</name>

 <summary>GUI for multiple sequence alignment and molecular phylogeny</summary>

 <description>

<p>SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny.</p>

<ul>

	<li>SeaView reads and writes various file formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP,

	MASE, Newick) of DNA and protein sequences and of phylogenetic trees.</li>

	<li>SeaView drives programs muscle or Clustal-Omega for multiple sequence alignment, 

	and also allows to use any external alignment algorithm able to read and write FASTA-formatted files.</li>

	<li>Seaview drives the Gblocks program to select blocks of evolutionarily conserved sites.</li>

	<li>SeaView computes phylogenetic trees by:</li>

	<li>- parsimony, using PHYLIP's dnapars/protpars algorithm,</li>

	<li>- distance, with NJ or BioNJ algorithms on a variety of evolutionary distances,</li>

	<li>- maximum likelihood, driving program PhyML 3.1.</li>

	<li>SeaView prints and draws phylogenetic trees on screen, SVG, PDF or PostScript files.</li>

	<li>SeaView allows to download sequences from EMBL/GenBank/UniProt using the Internet.</li>

</ul>

 </description>

 <screenshots>

  <screenshot type="default">

   <image>http://doua.prabi.fr/binaries/seaview4.png</image>

   <caption>The main alignment window used in the color-by-codon mode</caption>

  </screenshot>

  <screenshot>

   <image>http://doua.prabi.fr/binaries/seaview-tree.png</image>

   <caption>The tree window with some zoom-in applied</caption>

  </screenshot>

  <screenshot>

   <image>  http://doua.prabi.fr/software/seaview_data/PhyML-dialog.png</image>

   <caption>Dialog window to perform Maximum-Likelihood tree-building</caption>

  </screenshot>

 </screenshots>

 <url type="homepage">http://doua.prabi.fr/software/seaview</url>

 <updatecontact>manolo.gouy_at_univ-lyon1.fr</updatecontact>

 <developer_name>Manolo Gouy</developer_name>

  <keywords>

  <keyword>molecular phylogeny</keyword>

  <keyword>phylogenetic tree</keyword>

  <keyword>sequence alignment</keyword>

  <keyword>parsimony</keyword>

  <keyword>neighbor-joining/keyword>

  <keyword>maximum likelihood</keyword>

  </keywords>

</component>